EQTN

Summary

EQTN (equatorin, HGNC:1359) is a protein-coding gene on chromosome 9p21.2, encoding Equatorin (Q9NQ60). Acrosomal membrane-anchored protein involved in the process of fertilization and in acrosome biogenesis.

Predicted to be involved in acrosomal vesicle exocytosis; endocytosis; and fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to act upstream of or within establishment of localization in cell. Predicted to be located in early endosome and nucleus. Predicted to be active in inner acrosomal membrane; outer acrosomal membrane; and plasma membrane.

Source: NCBI Gene 54586 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_020641

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1359
Approved symbol	EQTN
Name	equatorin
Location	9p21.2
Locus type	gene with protein product
Status	Approved
Aliases	AFAF, SPACA8, equatorin
Ensembl gene	ENSG00000120160
Ensembl biotype	protein_coding
OMIM	617653
Entrez	54586

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000380031, ENST00000380032, ENST00000484994, ENST00000537675

RefSeq mRNA: 2 — MANE Select: NM_020641 NM_001161585, NM_020641

CCDS: CCDS35001, CCDS55300

Canonical transcript exons

ENST00000380032 — 8 exons

Exon	Start	End
ENSE00000813552	27286209	27286362
ENSE00000813553	27289672	27289731
ENSE00000813554	27291019	27291063
ENSE00000813555	27292401	27292487
ENSE00000813556	27294316	27294402
ENSE00000813557	27296613	27296738
ENSE00001483487	27284654	27284972
ENSE00001483492	27296980	27297150

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 95.36.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0752 / max 59.9943, expressed in 4 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100328	0.0302	4
100329	0.0269	3
100330	0.0181	3

Top tissues by expression

236 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	95.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.87	gold quality
left testis	UBERON:0004533	90.65	gold quality
right testis	UBERON:0004534	90.40	gold quality
testis	UBERON:0000473	88.00	gold quality
adult organism	UBERON:0007023	71.55	gold quality
corpus callosum	UBERON:0002336	61.90	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	57.44	gold quality
ventricular zone	UBERON:0003053	57.09	gold quality
spinal cord	UBERON:0002240	55.86	gold quality
mucosa of stomach	UBERON:0001199	55.63	gold quality
left ovary	UBERON:0002119	55.27	gold quality
right lung	UBERON:0002167	52.83	gold quality
rectum	UBERON:0001052	52.67	gold quality
right ovary	UBERON:0002118	52.56	gold quality
ovary	UBERON:0000992	52.13	gold quality
mucosa of transverse colon	UBERON:0004991	50.68	gold quality
small intestine Peyer’s patch	UBERON:0003454	49.70	gold quality
tibial artery	UBERON:0007610	49.55	gold quality
popliteal artery	UBERON:0002250	49.40	gold quality
transverse colon	UBERON:0001157	49.31	gold quality
left uterine tube	UBERON:0001303	49.06	gold quality
tibial nerve	UBERON:0001323	49.02	gold quality
body of stomach	UBERON:0001161	48.97	gold quality
small intestine	UBERON:0002108	48.65	gold quality
left coronary artery	UBERON:0001626	48.46	gold quality
substantia nigra	UBERON:0002038	48.20	gold quality
body of pancreas	UBERON:0001150	48.00	gold quality
aorta	UBERON:0000947	47.84	gold quality
descending thoracic aorta	UBERON:0002345	47.70	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.58

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• A genome-wide association study finds that the chromosome 9p21 locus is a major cause of familial amyotrophic lateral sclerosis in the Finnish population. (PMID:20801718)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Eqtn	ENSMUSG00000028575
rattus_norvegicus	Eqtn	ENSRNOG00000026323

Protein

Protein identifiers

Equatorin — Q9NQ60 (reviewed: Q9NQ60)

Alternative names: Acrosome formation-associated factor

All UniProt accessions (1): Q9NQ60

UniProt curated annotations — full annotation on UniProt →

Function. Acrosomal membrane-anchored protein involved in the process of fertilization and in acrosome biogenesis.

Subunit / interactions. Interacts with SNAP25.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome membrane. Acrosome inner membrane. Acrosome outer membrane.

Tissue specificity. Isoform 1 is highly expressed in testis. Isoform 2 is expressed at low levels in skin and blood.

Post-translational modifications. Highly N- and O-glycosylated; contains sialic acid.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NQ60-1	1	yes
Q9NQ60-2	2
Q9NQ60-3	3

RefSeq proteins (2): NP_001155057, NP_065692* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029282	Eqtn/Afaf	Family

Pfam: PF15339

UniProt features (15 total): splice variant 3, sequence variant 3, topological domain 2, glycosylation site 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQ60-F1	59.20	0.10

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (2): 76, 143

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): GOBP_SINGLE_FERTILIZATION, GOCC_SECRETORY_GRANULE, GOBP_MEMBRANE_FUSION, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, GOBP_SECRETION, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_CALCIUM_ION_REGULATED_EXOCYTOSIS, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_ACROSOME_REACTION, GOBP_PLASMA_MEMBRANE_FUSION, GOBP_MEMBRANE_ORGANIZATION, GOBP_FERTILIZATION, GOBP_IMPORT_INTO_CELL

GO Biological Process (3): endocytosis (GO:0006897), fusion of sperm to egg plasma membrane involved in single fertilization (GO:0007342), acrosomal vesicle exocytosis (GO:0060478)

GO Molecular Function (0):

GO Cellular Component (6): inner acrosomal membrane (GO:0002079), outer acrosomal membrane (GO:0002081), plasma membrane (GO:0005886), acrosomal membrane (GO:0002080), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
acrosomal membrane	2
cytoplasmic vesicle membrane	2
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
single fertilization	1
cellular process involved in reproduction in multicellular organism	1
acrosome reaction	1
calcium-ion regulated exocytosis	1
membrane	1
cell periphery	1
acrosomal vesicle	1
secretory granule membrane	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

1270 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EQTN	MOB3B	Q86TA1	542
EQTN	FAM170B	A6NMN3	486
EQTN	TEX101	Q9BY14	461
EQTN	IZUMO1	Q8IYV9	442
EQTN	SPAM1	P38567	430
EQTN	CD9	P21926	426
EQTN	PATE4	P0C8F1	399
EQTN	GLT1D1	Q96MS3	396
EQTN	SPMIP6	Q8NCR6	395
EQTN	DEFB126	Q9BYW3	386
EQTN	CLGN	O14967	385
EQTN	ADAM30	Q9UKF2	382
EQTN	ADAM2	P78326	378
EQTN	NT5C1B	Q96P26	370
EQTN	CABYR	O75952	368
EQTN	MAN2A2	P49641	368

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A7H0DND5, A8DYY6, F5HGU6, F5HI32, H2KZ49, P06817, P16192, P16196, P16200, P16204, P16206, P16208, P27908, P33304, P33852, P34718, P36358, P46946, P55082, P67908, P67909, P68618, P68619, P69338, P69339, Q00682, Q03345, Q04922, Q05569, Q05611, Q06693, Q08729, Q09560, Q10034, Q20646, Q23647, Q2M2T8, Q5R9E4, Q5UQ18, Q5UQI5

Diamond homologs: Q2LCV6, Q9D9V2, Q9NQ60

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

60 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

819 predictions. Top by Δscore:

Variant	Effect	Δscore
9:27284973:C:CC	acceptor_gain	1.0000
9:27286204:CTTA:C	donor_loss	1.0000
9:27286205:TTACC:T	donor_loss	1.0000
9:27286206:TACC:T	donor_loss	1.0000
9:27286207:A:AC	donor_gain	1.0000
9:27286207:A:C	donor_loss	1.0000
9:27286208:C:CA	donor_gain	1.0000
9:27286208:CCT:C	donor_gain	1.0000
9:27286358:AGACT:A	acceptor_gain	1.0000
9:27286359:GACT:G	acceptor_gain	1.0000
9:27286361:CT:C	acceptor_gain	1.0000
9:27286361:CTCT:C	acceptor_loss	1.0000
9:27286363:C:CC	acceptor_gain	1.0000
9:27292399:A:AC	donor_gain	1.0000
9:27292400:C:CC	donor_gain	1.0000
9:27294400:CAT:C	acceptor_gain	1.0000
9:27296612:CATTG:C	donor_gain	1.0000
9:27284968:TATAA:T	acceptor_gain	0.9900
9:27284970:TAA:T	acceptor_gain	0.9900
9:27286207:AC:A	donor_gain	0.9900
9:27286208:CC:C	donor_gain	0.9900
9:27289729:TAG:T	acceptor_gain	0.9900
9:27289731:GC:G	acceptor_loss	0.9900
9:27289732:C:CC	acceptor_gain	0.9900
9:27289733:T:TC	acceptor_loss	0.9900
9:27289734:G:C	acceptor_loss	0.9900
9:27289741:CAAA:C	acceptor_loss	0.9900
9:27289742:A:T	acceptor_loss	0.9900
9:27292341:A:C	donor_gain	0.9900
9:27294398:CACAT:C	acceptor_gain	0.9900

AlphaMissense

1953 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:27284912:A:C	F232L	0.992
9:27284912:A:T	F232L	0.992
9:27284914:A:G	F232L	0.992
9:27291035:C:A	W135C	0.987
9:27291035:C:G	W135C	0.987
9:27284879:A:C	F243L	0.986
9:27284879:A:T	F243L	0.986
9:27284881:A:G	F243L	0.986
9:27291037:A:G	W135R	0.984
9:27291037:A:T	W135R	0.984
9:27286243:A:G	C201R	0.980
9:27294396:A:G	F70S	0.974
9:27291038:A:C	F134L	0.971
9:27291038:A:T	F134L	0.971
9:27291040:A:G	F134L	0.971
9:27294349:C:G	A86P	0.970
9:27286238:A:C	S202R	0.968
9:27286238:A:T	S202R	0.968
9:27286240:T:G	S202R	0.968
9:27284913:A:C	F232C	0.967
9:27291027:A:G	L138S	0.965
9:27286248:G:T	A199E	0.961
9:27294360:A:G	I82T	0.961
9:27291039:A:C	F134C	0.959
9:27291039:A:G	F134S	0.959
9:27294354:A:T	V84E	0.958
9:27291019:C:G	A141P	0.957
9:27286291:C:G	G185R	0.954
9:27286291:C:T	G185R	0.954
9:27294360:A:T	I82K	0.953

dbSNP variants (sampled 300 via entrez): RS1000009159 (9:27297884 T>C), RS1000151836 (9:27290900 G>A,C), RS1000236109 (9:27287160 C>G), RS1000246030 (9:27287390 A>T), RS1000573482 (9:27288561 C>T), RS1000579643 (9:27287784 A>G), RS1000706511 (9:27297936 G>A,C,T), RS1001195276 (9:27298214 A>G), RS1001219407 (9:27296804 T>C), RS1001303804 (9:27292815 T>C), RS1001450592 (9:27287525 C>T), RS1001530510 (9:27286286 G>A,T), RS1001565255 (9:27291852 C>T), RS1001582849 (9:27286526 A>G), RS1001859208 (9:27287789 T>C)

Disease associations

OMIM: gene MIM:617653 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001762_81	Obesity-related traits	6.000000e-06
GCST003831_45	Asthma	7.000000e-10
GCST003831_47	Asthma	2.000000e-08
GCST003833_23	Adult asthma	3.000000e-07
GCST003833_24	Adult asthma	2.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases methylation, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Antirheumatic Agents	increases expression	1
Particulate Matter	decreases methylation, increases abundance	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.